#ifndef	_COMPARE_SEQS_H_
#define	_COMPARE_SEQS_H_

/*
 * Defines the data needed for comparison of an input sequence and the reference sequence.
 * Note that we already know that the frist minMatchLength chars are the same.
 */
struct CompareSeqs
{
	// The input sequence
	InputSequence *inSeq;

	// The position where the comparison begins in the input sequence
	size_t inputPos;

	// The positions where the comparison should start in the reference sequence (in a DynmaicBitset)
	const DynamicBitset *refPositions;

	// C'tor - receives the input sequence position from which we need to compare against reference positions in a given DynamicBitset
	CompareSeqs(InputSequence *_inSeq, size_t _inputPos, const DynamicBitset *_refPositions) :
		inSeq(_inSeq), inputPos(_inputPos), refPositions(_refPositions)
	{ }
};

#endif	/* _COMPARE_SEQS_H_ */

